Auto importing from multiple folders and sub-folders

I am trying to import files from my PDF local library which is organised in multiple folders and subfolders already. To my surprise I realised that the auto-import feature of Endnote can only handle PDFs immediately under one folder only! This should be a very simple feature already there in Mendeley for a long time which enables importing and updating existing local pdf libraries organised in multuple folders with a single click. I cannot see the reason why the auto-import folder cannot see the contained subfolders.